Skip to main content
ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #373038

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: A metagenomics approach to study pecan bacterial leaf scorch disease associated with Xylella fastidiosa in Georgia

item Chen, Jianchi
item HUANG, J - South China Agricultural Univerisity
item BAO, M - South China Agricultural Univerisity
item Hotchkiss, Michael - Mike
item Bock, Clive

Submitted to: American Phytopathological Society Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 8/3/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Pecan bacterial leaf scorch disease (PBLSD), caused by Xylella fastidiosa (Xf), is endemic to pecan in the southern USA. Research is challenging as Xf is difficult to culture and pecan is a woody perennial. Total leaf DNA was extracted from 40 suspect PBLSD samples from 3 orchards in Georgia. Xf was detected by SYBR green rt-PCR with 2 primer sets, A: Teme150fc-Teme454rg specific to subsp. fastidiosa, and B: Dixon454fa-Dixon1261rg specific to subsp. multiplex. Only 2 samples (1 site, 1 tree each of cvs. Elliott and Forkert) were confirmed (Ct<30) as subsp. fastidiosa, and 19 samples (2 sites, several trees of cvs. Cape Fear and Candy) as subsp. multiplex. Two samples, T1 (cv. Elliott; subsp. fastidiosa - Ct=25.62 for set A and Ct=35.18 for set B) and T9 (cv. Cape Fear; subsp. multiplex - Ct=32.64 for set A and Ct=21.89 for set B), were selected for high throughput sequencing (Illumina HiSeq 3000). Over 300 M short reads (101 bp each; >30 Gbp data) were generated from each sample. A partial genome (10,338 bp) was obtained from T1 referenced to the whole genome sequence (WGS) of strain M23 (NC_010577.1, subsp. fastidiosa). A close to complete genome (2,322,390 bp) was obtained from T9 referenced to the WGS of strain M12 (NC_010513.1, subsp. multiplex). Thus, PCR and genome sequence analyses shows both Xf subsps. fastidiosa and multiplex are associated with PBLSD, but subsp. multiplex is dominant in the studied samples. Metagenomic analyses (using software Kaiju) also detected other bacterial and fungal endophytes in the two samples.